Multiple sequence alignment - TraesCS2A01G059600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G059600 chr2A 100.000 4316 0 0 1 4316 25465461 25469776 0.000000e+00 7971.0
1 TraesCS2A01G059600 chr2A 97.939 2766 45 6 1 2755 25452078 25454842 0.000000e+00 4782.0
2 TraesCS2A01G059600 chr2A 98.998 1497 15 0 2820 4316 25455259 25456755 0.000000e+00 2682.0
3 TraesCS2A01G059600 chr2A 79.699 266 28 12 4021 4265 25451073 25451333 7.420000e-38 169.0
4 TraesCS2A01G059600 chr2A 91.429 70 4 2 3371 3439 25455736 25455804 1.280000e-15 95.3
5 TraesCS2A01G059600 chr2A 91.304 69 6 0 3371 3439 25468757 25468825 1.280000e-15 95.3
6 TraesCS2A01G059600 chr2A 91.304 69 6 0 3297 3365 25468831 25468899 1.280000e-15 95.3
7 TraesCS2A01G059600 chr2A 95.238 42 2 0 1707 1748 25453625 25453666 2.790000e-07 67.6
8 TraesCS2A01G059600 chr2A 95.238 42 2 0 1541 1582 25453791 25453832 2.790000e-07 67.6
9 TraesCS2A01G059600 chr2A 95.238 42 2 0 1707 1748 25467001 25467042 2.790000e-07 67.6
10 TraesCS2A01G059600 chr2A 95.238 42 2 0 1541 1582 25467167 25467208 2.790000e-07 67.6
11 TraesCS2A01G059600 chr2D 93.881 1618 78 13 156 1759 23315375 23313765 0.000000e+00 2420.0
12 TraesCS2A01G059600 chr2D 92.181 243 14 3 1681 1919 23313909 23313668 5.350000e-89 339.0
13 TraesCS2A01G059600 chr2D 92.958 142 8 1 867 1006 23313667 23313526 5.660000e-49 206.0
14 TraesCS2A01G059600 chr2D 96.512 86 3 0 1 86 23316185 23316100 4.500000e-30 143.0
15 TraesCS2A01G059600 chr2D 87.500 64 6 2 1541 1604 23313883 23313822 5.990000e-09 73.1
16 TraesCS2A01G059600 chr2B 90.837 1266 76 17 1644 2891 36973313 36974556 0.000000e+00 1659.0
17 TraesCS2A01G059600 chr2B 95.706 978 35 4 2889 3860 36974581 36975557 0.000000e+00 1567.0
18 TraesCS2A01G059600 chr2B 85.315 967 107 17 542 1483 36971751 36972707 0.000000e+00 966.0
19 TraesCS2A01G059600 chr2B 94.000 200 11 1 4099 4298 36977642 36977840 7.010000e-78 302.0
20 TraesCS2A01G059600 chr2B 86.364 220 19 4 3859 4067 36977422 36977641 3.360000e-56 230.0
21 TraesCS2A01G059600 chr2B 91.111 45 4 0 1774 1818 36972985 36973029 1.300000e-05 62.1
22 TraesCS2A01G059600 chr1A 76.780 646 136 13 2183 2818 2550595 2551236 2.470000e-92 350.0
23 TraesCS2A01G059600 chr4A 89.706 68 5 2 351 418 67315920 67315855 7.690000e-13 86.1
24 TraesCS2A01G059600 chr7B 84.810 79 9 3 341 418 585519680 585519756 4.630000e-10 76.8
25 TraesCS2A01G059600 chr4D 86.765 68 9 0 351 418 386145010 386144943 4.630000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G059600 chr2A 25465461 25469776 4315 False 1659.360000 7971 94.616800 1 4316 5 chr2A.!!$F2 4315
1 TraesCS2A01G059600 chr2A 25451073 25456755 5682 False 1310.583333 4782 93.090167 1 4316 6 chr2A.!!$F1 4315
2 TraesCS2A01G059600 chr2D 23313526 23316185 2659 True 636.220000 2420 92.606400 1 1919 5 chr2D.!!$R1 1918
3 TraesCS2A01G059600 chr2B 36971751 36977840 6089 False 797.683333 1659 90.555500 542 4298 6 chr2B.!!$F1 3756
4 TraesCS2A01G059600 chr1A 2550595 2551236 641 False 350.000000 350 76.780000 2183 2818 1 chr1A.!!$F1 635

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
94 1100 0.517316 GGCAACAGGTAGTTTCAGCG 59.483 55.000 0.00 0.0 38.74 5.18 F
443 2143 1.603802 CCACTGCTTTGTAGTGTGTGG 59.396 52.381 13.09 0.0 43.02 4.17 F
1955 4149 1.250154 CCCGATGTGCCAACACCAAT 61.250 55.000 0.00 0.0 46.86 3.16 F
2292 4490 4.021104 TCGAGCTGAAATGAGTATATGGGG 60.021 45.833 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 4149 2.429610 GGTGCATCGGTTAACTCCTAGA 59.570 50.00 5.42 0.0 0.00 2.43 R
2412 4610 7.603784 ACTTCTTGAAAAGCATTTGAGTTTGTT 59.396 29.63 0.00 0.0 45.70 2.83 R
2949 5540 1.071314 ACACCACCCAATCCCCAGAA 61.071 55.00 0.00 0.0 0.00 3.02 R
3993 8467 0.322816 GAGCCTGCATCAGAAACCCA 60.323 55.00 0.00 0.0 32.44 4.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 1100 0.517316 GGCAACAGGTAGTTTCAGCG 59.483 55.000 0.00 0.00 38.74 5.18
172 1871 5.795766 ACAATTATTGAGCGACACGTATTG 58.204 37.500 12.28 0.00 0.00 1.90
184 1883 5.070862 CGACACGTATTGTTGAAAGTAAGC 58.929 41.667 0.00 0.00 41.77 3.09
217 1916 7.765819 GGCATAGTTAAAGCTTTCATGGAAAAT 59.234 33.333 16.57 5.16 30.84 1.82
443 2143 1.603802 CCACTGCTTTGTAGTGTGTGG 59.396 52.381 13.09 0.00 43.02 4.17
684 2392 2.423185 GCGGATCATCACAACCATTCAA 59.577 45.455 0.00 0.00 0.00 2.69
1286 3019 6.238759 GGCCCATTAGACATTAGAACAACATC 60.239 42.308 0.00 0.00 0.00 3.06
1507 3444 6.478129 TCGTAACAGGAGGAAATATTTGGTT 58.522 36.000 5.17 3.48 0.00 3.67
1955 4149 1.250154 CCCGATGTGCCAACACCAAT 61.250 55.000 0.00 0.00 46.86 3.16
2292 4490 4.021104 TCGAGCTGAAATGAGTATATGGGG 60.021 45.833 0.00 0.00 0.00 4.96
2412 4610 9.320295 TCATGTACATACATATCACCCATTCTA 57.680 33.333 8.32 0.00 44.57 2.10
2949 5540 4.955811 TTGTATACTGCAGGATCCGAAT 57.044 40.909 16.72 0.00 0.00 3.34
3063 5654 2.242043 CAAGCCCTGACAGGATTTGTT 58.758 47.619 23.77 5.61 41.05 2.83
3390 5981 7.825331 TCTACAAATGGTTGTATTGGTTGAA 57.175 32.000 0.10 0.00 46.57 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 1100 9.832445 TCCAACTTATTTATTACTGGACTCATC 57.168 33.333 0.00 0.00 0.00 2.92
172 1871 3.234386 GCCATGTTCGCTTACTTTCAAC 58.766 45.455 0.00 0.00 0.00 3.18
184 1883 4.882671 AGCTTTAACTATGCCATGTTCG 57.117 40.909 0.00 0.00 0.00 3.95
315 2015 3.609373 CCAATCATGTCGCACAACATTTC 59.391 43.478 0.00 0.00 37.78 2.17
443 2143 4.341520 CCTAGGTACCAACATACACTCTCC 59.658 50.000 15.94 0.00 0.00 3.71
514 2214 1.035932 TAGGACGAGTGCCACCTAGC 61.036 60.000 0.00 0.00 34.42 3.42
617 2318 5.587443 TCAGTTGCTCCATCAATATTCACTG 59.413 40.000 0.00 0.00 0.00 3.66
730 2438 7.182026 TCCTGGTTTTTCAGATAAGGAGATACA 59.818 37.037 0.00 0.00 36.93 2.29
810 2522 9.838339 TGATCTTATCTTTCTTTGGATAAGGAC 57.162 33.333 17.18 13.23 45.31 3.85
1955 4149 2.429610 GGTGCATCGGTTAACTCCTAGA 59.570 50.000 5.42 0.00 0.00 2.43
2292 4490 7.730364 TGAGAGTTTTCTTGATTAGGTGAAC 57.270 36.000 0.00 0.00 32.53 3.18
2412 4610 7.603784 ACTTCTTGAAAAGCATTTGAGTTTGTT 59.396 29.630 0.00 0.00 45.70 2.83
2949 5540 1.071314 ACACCACCCAATCCCCAGAA 61.071 55.000 0.00 0.00 0.00 3.02
3063 5654 9.523168 GGGCCATGTGTATTATTTAGGTAATTA 57.477 33.333 4.39 0.00 0.00 1.40
3390 5981 2.919228 AGGCGAGAAAAACTTGTGTCT 58.081 42.857 0.00 0.00 32.82 3.41
3993 8467 0.322816 GAGCCTGCATCAGAAACCCA 60.323 55.000 0.00 0.00 32.44 4.51


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.